X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=b393194bbc3a4c89fd2ae8ea3f7f7ba67f84b927;hb=9ada98592a54c82d08f3d46c9b1d8c3e472a922d;hp=de6004d7e387d0e241dfbc205695d359dbcf6dda;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index de6004d..b393194 100644
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -32,28 +32,8 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
 			refSeqs = getBlastSeqs(query, numWanted);
 		}
 		
-//ofstream out;
-//string name = toString(numi+1); 
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(0, name.find_last_of("|"));
-//cout << name << endl;
-//string filename = name + ".seqsformaligner";
-//openOutputFile(filename, out);	
-//for (int u = 0; u < refSeqs.size(); u++) {  refSeqs[u]->printSequence(out);	}
-//out.close();
-//filename = name + ".fasta";
-//openOutputFile(filename, out);	
-//query->printSequence(out);
-//out.close();
-
-//for (int i = 0; i < refSeqs.size(); i++)  { cout << refSeqs[i]->getName() << endl;  }	
-//cout << "before = " << refSeqs.size() << endl;
 		refSeqs = minCoverageFilter(refSeqs);
-//cout << "after = " << refSeqs.size() << endl;		
+		
 		if (refSeqs.size() < 2)  { 
 			for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];	}
 			percentIdenticalQueryChimera = 0.0;
@@ -61,7 +41,7 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
 		}
 		
 		int chimeraPenalty = computeChimeraPenalty();
-//cout << chimeraPenalty << endl;		
+	
 		//fills outputResults
 		chimera = chimeraMaligner(chimeraPenalty, decalc);
 		
@@ -500,8 +480,7 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
 }
 //***************************************************************************************************************
 vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
-	try {
-cout << q->getName() << endl;	
+	try {	
 		//generate blastdb
 		Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty);
 		for (int i = 0; i < db.size(); i++) { 	database->addSequence(*db[i]);	}
@@ -509,55 +488,42 @@ cout << q->getName() << endl;
 		database->setNumSeqs(db.size());
 		
 		//get parts of query
-		string queryAligned = q->getAligned();
-		string leftQuery = queryAligned.substr(0, (queryAligned.length() / 3)); //first 1/3 of the sequence
-		string rightQuery = queryAligned.substr(((queryAligned.length() / 3)*2)); //last 1/3 of the sequence
-		
+		string queryUnAligned = q->getUnaligned();
+		string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
+		string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
+
 		Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
 		Sequence* queryRight = new Sequence(q->getName(), rightQuery);
 		
-		map<int, float> tempIndexesRight = database->findClosest(queryRight, num);
-		map<int, float> tempIndexesLeft = database->findClosest(queryLeft, num);
-		
-		//merge results
-		vector<rank> mergedResults;
+		vector<int> tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1);
+		vector<int> tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1);
 		
-		map<int, float>::iterator it;
-		map<int, float>::iterator it2;
+		//merge results		
+		map<int, int> seen;
+		map<int, int>::iterator it;
 		
-		//add in right guys merging common finds
-		for (it = tempIndexesRight.begin(); it != tempIndexesRight.end(); it++) {
-			it2 = tempIndexesLeft.find(it->first);
-			
-			if (it2 == tempIndexesLeft.end()) {  //result only present in right
-				rank temp(it->first, it->second);
-				mergedResults.push_back(temp); 
+		vector<int> mergedResults;
+		for (int i = 0; i < tempIndexesLeft.size(); i++) {
+			//add left if you havent already
+			it = seen.find(tempIndexesLeft[i]);
+			if (it == seen.end()) {  
+				mergedResults.push_back(tempIndexesLeft[i]);
+				seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
+			}
 
-			}else { //result present in both save best score
-				float bestscore;
-				if (it->second > it2->second)	{  bestscore = it->second;  }
-				else							{  bestscore = it2->second; }
-				
-				rank temp(it->first, bestscore);
-				mergedResults.push_back(temp);
-				
-				tempIndexesLeft.erase(it2);
+			//add right if you havent already
+			it = seen.find(tempIndexesRight[i]);
+			if (it == seen.end()) {  
+				mergedResults.push_back(tempIndexesRight[i]);
+				seen[tempIndexesRight[i]] = tempIndexesRight[i];
 			}
 		}
 		
-		//add in unique left guys
-		for (it = tempIndexesLeft.begin(); it != tempIndexesLeft.end(); it++) {
-			rank temp(it->first, it->second);
-			mergedResults.push_back(temp); 
-		}
-		
-		sort(mergedResults.begin(), mergedResults.end(), compareMembers);
 		
 		vector<Sequence*> refResults;
 		for (int i = 0; i < numWanted; i++) {
-			Sequence* temp = new Sequence(db[mergedResults[i].num]->getName(), db[mergedResults[i].num]->getAligned());
+			Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
 			refResults.push_back(temp);
-cout << db[mergedResults[i].num]->getName() << endl;
 		}
 		
 		delete queryRight;